welcome to the site!
First things first, remove the spectre air filter and return the airbox back to stock with the lid and everything. GM suprisingly gave us a well flowing factory cold air intake that filters excellently. If you want more flow, like said above, Leroydiesel.com sells a high flow filter that will allow you to keep using the airbox as intended, but with more airflow.
Secondly, I see you are missing the filter restriction indicator. Replace Immediately!!!
IDK if the vaccum values are the same, but one off a 96+ vortec gasser would at least fit the hole properly and plug it.
As of right now, with nothing in that hole, you are sucking dirt!!!!!
3rd, like said above, return the turbo back to vaccum control. Your mpg will improve and the computer will be happy. If you are going all out with it, no use wasting money going too far with the OEM turbo, save up your $ for a big housing turbo. Alot of guys love the ATT, and it is sold by Leroydiesel.com
If you are in a hurry and needed it yesterday, the dealer is a good place for o-rings for the fuel system, they will be correct, but will not be cheap. If you had a bit of time to allow freighting some in, Leroydiesel.com sells a o-ring kit for the filter housing.
You may have messed up changing the o-ring on the optical sensor, as the OS needs to be precisely located, I believe to properly replace it, one needs to send it off to a pump shop and have them dial in the new sensor via a test stand. Time will tell though.
As a new 6.5L owner, make certain to inspect the harmonic damper and the oil cooler lines. Many a good 6.5L have been killed by either of those going bad, so its quite important.
I like the stainless oil cooler lines and Fluidampr from Leroydiesel, but if you are trying to fix it on a budget, I would go with no less than GM oil cooler lines.
IIRC the cost of the factory GM big lines on the 97+ piston jet cooling blocks will exceed the cost of Leroy's lines, so that makes it a no-brainer to go with Leroy's. On a 95 with the small ports that I was fixing on a budget for re-sale, I went with some GM lines and they were cheap. made in china, and probably gonna leak in less than 5 years, but better than what was on there.
For a budget damper, a AC Delco off Rockauto.com would be my first choice.
If you have ANY question related to your pickup, feel free to ask. Many folks on this forum are happy and willing to help, and enjoy helping someone fix an issue without wasting a dime.
I know that thanks to these forums, I have learned the 6.5L enough to have excellent luck with them, not making hardly any mistakes, because someone before me has made such mistakes and has learned from them, and was nice enough to pass on the info to save future owners time, money, and grief.
Good luck and welcome to the site!